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[ENH] BEP031: Microscopy #881

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95787ec
Initial commit adding Microscopy related files
mariehbourget Sep 16, 2021
b83a72d
Add Link descriptions and fix md formatting
mariehbourget Sep 16, 2021
8e29cd8
Fix md formatting
mariehbourget Sep 20, 2021
ec29dcd
Move "chunk" entity at the end of filename before modality_suffix
mariehbourget Sep 28, 2021
5e092ca
Add link to OME-TIFF dataset
mariehbourget Sep 30, 2021
d4449af
Update src/04-modality-specific-files/10-microscopy.md
mariehbourget Sep 30, 2021
b8ad766
Apply suggestions from code review
mariehbourget Oct 1, 2021
2a5cf25
Update "TissueDeformationScaling" field and JSON example
mariehbourget Oct 1, 2021
a133357
Update "uCT" suffix in schema/datatypes/microscopy.yaml
mariehbourget Oct 1, 2021
7f39d4c
Add res-label example
mariehbourget Oct 1, 2021
3ca5bca
Add "mm" and "nm" to PixelSizeUnits
mariehbourget Oct 8, 2021
a63b5b7
Update "Recommended participant data" after merge of PR #816
mariehbourget Oct 15, 2021
f9c2125
Resolve conflict with master for entities.yaml
mariehbourget Oct 16, 2021
169e4da
Merge branch 'master' into bep031
mariehbourget Oct 16, 2021
b2e1f8a
Update entities.yaml in objects and rules schema folders
mariehbourget Oct 16, 2021
7a904be
Update microscopy.yaml datatypes rules schema folder
mariehbourget Oct 16, 2021
32496fd
Apply suggestions from code review
mariehbourget Oct 27, 2021
711fdac
Fix md formatting
mariehbourget Oct 27, 2021
c33c6f6
Make protocols.io an example in SampleExtractionProtocol and
mariehbourget Oct 28, 2021
8ccf4de
Re-wording of chunk-index section and chunk transformation matrix is
mariehbourget Nov 4, 2021
cab50db
Fix typos
mariehbourget Nov 4, 2021
a4a5771
Fix wording
mariehbourget Nov 9, 2021
c66687f
Fix tif extension in src/schema/rules/datatypes/microscopy.yaml
mariehbourget Nov 12, 2021
ed408c1
Remove duplicated text in stain-label description
mariehbourget Nov 12, 2021
b95163a
Correction of the name of "Fluorescence" modality to "Fluorescence mi…
mariehbourget Nov 12, 2021
6c595ca
Add figure and example for chunk transformation
mariehbourget Nov 12, 2021
f4c16fc
Update src/04-modality-specific-files/10-microscopy.md
mariehbourget Nov 13, 2021
545b195
Update README.md
mariehbourget Nov 15, 2021
e077186
Add full OME-NGFF name
mariehbourget Nov 15, 2021
e65b7f4
Correction
mariehbourget Nov 15, 2021
bfb027b
Fix formatting
mariehbourget Nov 15, 2021
60ecb3d
Make BodyPartDetails RECOMMENDED
mariehbourget Nov 16, 2021
d93aab9
Update src/04-modality-specific-files/10-microscopy.md
mariehbourget Nov 16, 2021
c3dad74
Clarify stain-label and SampleStaining text in Filename entities section
mariehbourget Nov 16, 2021
dca2763
Update examples with real modality_suffix and file extensions
mariehbourget Nov 16, 2021
ac49f2d
Clarify text of chunk-index and chunk transformation
mariehbourget Nov 16, 2021
ab149a5
Update BodyPartDetailsOntology as URI
mariehbourget Nov 16, 2021
fd75df8
Correction to SampleEnvironment values
mariehbourget Nov 16, 2021
3d50db2
Fix md formatting
mariehbourget Nov 16, 2021
ffa7088
Add mention that "session" is optional
mariehbourget Nov 18, 2021
c735f31
wording: replace some "can" with "MAY" or "MUST"
mariehbourget Nov 18, 2021
9a23a8b
Clarification on participants.tsv file
mariehbourget Nov 18, 2021
0055ad6
Correction to stain description in entities.yml
mariehbourget Nov 19, 2021
f067bc4
Update src/02-common-principles.md
mariehbourget Nov 23, 2021
7edf319
10-microscpy.md: Change "microscopy" data type for "micr"
mariehbourget Nov 23, 2021
8414e89
Update datatype micr.yaml in schema and fix macro in entity table
mariehbourget Nov 23, 2021
f280aba
Clarify usage of samples/participants tsv/json files
mariehbourget Nov 23, 2021
1ec7905
Correction to "ex vivo" in JSON example
mariehbourget Nov 23, 2021
00abe1d
Correction samples/participants tsv/json file sections
mariehbourget Nov 23, 2021
d530845
Merge branch 'master' into bep031
mariehbourget Nov 26, 2021
886fd14
Implement macros for examples
mariehbourget Nov 29, 2021
44e6992
Correction: replace <modality_suffix> by <suffix>
mariehbourget Nov 29, 2021
a7e34a3
Add microscopy to schema/objects/datatypes.yaml
mariehbourget Nov 30, 2021
c778029
Add microscopy suffixes to schema/objects/suffixes.yaml
mariehbourget Nov 30, 2021
5978a95
Add microscopy to schema/rules/modalities.yaml
mariehbourget Nov 30, 2021
a6d6ece
Add make_filename_template MACROs
mariehbourget Nov 30, 2021
de73132
Add make_suffix_table MACRO
mariehbourget Nov 30, 2021
68b9128
Add microscopy json metadata to schema/objects/metadata.yaml
mariehbourget Dec 2, 2021
a1bd2a0
Add metadata table macros to 10-microscopy.md
mariehbourget Dec 2, 2021
202d507
Adjust StationName definition in 01-magnetic-resonance-imaging-data.md
mariehbourget Dec 2, 2021
9376c72
Adjust BodyPart definition in 09-positron-emission-tomography.md
mariehbourget Dec 2, 2021
f13ed59
Change "recording data" for "imaging data"
mariehbourget Dec 2, 2021
48d9ba9
Remove unused link definitions
mariehbourget Dec 2, 2021
877e920
Clarify samples/participants sections
mariehbourget Dec 3, 2021
79091c9
schema/objects/metadata.yaml: Apply review suggestions and add
mariehbourget Dec 3, 2021
7b63f8e
Address BEP031 macro requests (#945)
tsalo Dec 3, 2021
c303ce4
Update src/schema/objects/metadata.yaml
mariehbourget Dec 3, 2021
8691bfa
Update names of bids-examples datasets
mariehbourget Dec 6, 2021
c264f74
Remove comments about filename templates
mariehbourget Dec 6, 2021
fbea131
Remove comments for modality suffix table
mariehbourget Dec 6, 2021
7f3b35d
Apply suggestions from code review
mariehbourget Dec 20, 2021
ed19ddd
Update BIDS-examples link and remove commented lines
mariehbourget Jan 13, 2022
8062d19
Add "samples" to src/schema/objects/top_level_files.yaml
mariehbourget Jan 13, 2022
5a58d60
Formatting in src/schema/objects/top_level_files.yaml
mariehbourget Jan 13, 2022
c84691c
Merge remote-tracking branch 'upstream/master' into bep031
effigies Jan 13, 2022
b0b144b
Fix link to sessions file in src/schema/objects/top_level_files.yaml
mariehbourget Jan 17, 2022
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1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ BIDS currently supports the following data modalities with more to come in the f
- behavioral
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- physiological
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- PET
- microscopy

# Formatting your data with BIDS

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1 change: 1 addition & 0 deletions mkdocs.yml
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Expand Up @@ -39,6 +39,7 @@ nav:
- Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
- Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
- Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
- Microscopy: 04-modality-specific-files/10-microscopy.md
- Derivatives:
- BIDS Derivatives: 05-derivatives/01-introduction.md
- Common data types and metadata: 05-derivatives/02-common-data-types.md
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1 change: 1 addition & 0 deletions src/02-common-principles.md
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Expand Up @@ -56,6 +56,7 @@ misunderstanding we clarify them here.
1. `ieeg` (intracranial electroencephalography)
1. `beh` (behavioral)
1. `pet` (positron emission tomography)
1. `micr` (microscopy)

Data files are contained in a directory named for the data type.
In raw datasets, the data type directory is nested inside subject and
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Expand Up @@ -17,7 +17,7 @@ by Ben Inglis.
"Manufacturer": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0070 `Manufacturer`."),
"ManufacturersModelName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`."),
"DeviceSerialNumber": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`."),
"StationName": "RECOMMENDED",
"StationName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1010 `Station Name`."),
"SoftwareVersions": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 1020 `Software Versions`."),
"HardcopyDeviceSoftwareVersion": "DEPRECATED",
"MagneticFieldStrength": "RECOMMENDED, but REQUIRED for Arterial Spin Labeling",
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Expand Up @@ -143,7 +143,7 @@ which we divide into several categories:
"InstitutionName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0080 `InstitutionName`."),
"InstitutionAddress": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`."),
"InstitutionalDepartmentName": ("RECOMMENDED", "Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`."),
"BodyPart": "RECOMMENDED",
"BodyPart": ("RECOMMENDED", "Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`."),
}
) }}

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